6T74

New antiparallel dimer of aureochrome 1a LOV domain mutants from Phaeodactylum tricornutum


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5A8B 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7291.15in 1.1 M sodium malonate, 0.1 M HEPES pH 7.0, 0.5 % Jeffamine ED-2003 under dark conditions

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.746α = 90
b = 100.746β = 90
c = 120.57γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-05-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.00SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.946.5299.960.012320.017420.01232124.5124947638.84
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)R Split (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.9681000.29190.41280.29190.8380.29192.392

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5a8b1.946.5246990248699.910.15380.1748RANDOM44.958
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.89-0.891.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.033
r_dihedral_angle_4_deg18.595
r_dihedral_angle_3_deg13.108
r_dihedral_angle_1_deg6.423
r_angle_refined_deg1.652
r_angle_other_deg1.461
r_chiral_restr0.081
r_bond_refined_d0.011
r_gen_planes_refined0.011
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.033
r_dihedral_angle_4_deg18.595
r_dihedral_angle_3_deg13.108
r_dihedral_angle_1_deg6.423
r_angle_refined_deg1.652
r_angle_other_deg1.461
r_chiral_restr0.081
r_bond_refined_d0.011
r_gen_planes_refined0.011
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2205
Nucleic Acid Atoms
Solvent Atoms323
Heterogen Atoms131

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
REFMACrefinement
XDSdata scaling
MOLREPphasing